Author	SHA1	Message	Date
pat-s	5c4cca6cce	fix: verify the metadata database certificate with sslmode=verify-full (#235) ... Part of https://codefloe.com/rpkgs/bincraft/issues/225. Stacked on #234. Every connection to the metadata database used `sslmode = 'require'`, which encrypts but does not authenticate the server, so anyone able to impersonate `r-binaries.devxy.io:15432` would receive `PGPASS`. ## Changes - `.crow/build-all-versions.yaml`, `process-updates.yaml`, `prune-stale-flat-binaries.yaml`, `reindex.yaml`, `weekly-rebuild-reindex.yaml`: `metadata_db_sslmode = 'verify-full'` in every bincraft call. - `local/*.R`: the same for bincraft calls; scripts that call `DBI::dbConnect()` directly also pass `sslrootcert = bincraft::postgres_sslrootcert("verify-full")`, because libpq looks for `~/.postgresql/root.crt` rather than the system trust store. - `README.md`: note that the endpoint serves a Let's Encrypt certificate and how to verify it. - air reformatted three `=` assignments to `<-` in `local/missing-cran-packages-db.R` and `local/packages-without-any-binary.R` while the hook ran on those files. ## Ordering: merge last 1. devxy/k8s-talos#417 must be live: today the server presents an in-cluster certificate from a private CA, which `verify-full` rejects. 2. https://codefloe.com/rpkgs/bincraft/pulls/226 must be released: `local/install-bincraft.R` installs the latest tag, and older releases neither pass a root certificate nor export `postgres_sslrootcert()`. 3. #234 must be merged. Merging early fails every database connection in CI, and since #234 per-minor reindex failures fail the pipeline. Reviewed-on: #235	2026-10-17 07:45:46 +00:00
pat-s	4b7dc28cc8	feat(rebuild): shard the weekly rebuild and make each shard resumable (#163) ... ## Problem `weekly-rebuild-missing` runs one job per `<os>-<arch>` and walks that slot's list serially in a single `R -q -e` argument. That was cheap while every source fallback was skipped as "already built". Since bincraft #105/#106/#107 and #159 the gate works, and the lists are large: 8 917 source-served records on `amd64/alpine324`, 15 023 on `amd64/resolute`. Pipeline 10910 (`weekly_rebuild_missing:alpine-324-amd64`) ran for two days, reached `[8692/23885] cholera`, and was killed there. Two failures follow from that shape: - **No parallelism.** The work is embarrassingly parallel across packages; one job does all of it. - **No resumability and no clean stopping point.** The loop ends only by exhausting the list, so the only way to stop it is a kill. A restart re-walks from the first entry, paying a CRAN version resolution and an S3 `HEAD` per package before reaching new work. And a kill matches neither `success` nor `failure`, so the `Purge CDN cache` step never ran: the ~4 600 binaries 10910 did publish stayed hidden behind stale edge copies. ## What this changes **Three shards per slot.** Each of the 18 `OS`/`ARCH` rows gains `SPLIT_INTO`/`SPLIT_INDEX`, mirroring `build-all-versions.yaml`. Cron and manual routing are unchanged: both filters already match on `${OS}-${ARCH}`, so they now match all three shards of a slot. **`local/rebuild-missing.R`** replaces the ~1 500-character inline one-liner. The slice is interleaved rather than contiguous, because the list is alphabetical and cost clusters by name (`Rcpp*`, `Bioc*`, `rstan*`). **Resume by re-deriving state from the bucket.** One `s3_dir_info()` listing gives ETags for the slot; a package is outstanding iff its object's ETag equals CRAN's published `MD5sum`, i.e. it is still byte-identical to CRAN's source. That is `check_s3_root_package()` evaluated in bulk. No progress file, no volume, no DB cursor, and correct when a sibling shard or a `process-updates` run completes something concurrently. It reads ETags rather than the index's `Built` field the way `packages-to-build.R` does, because the index is no longer rewritten until the dependent pipeline runs and so cannot reflect the current run's progress. Unknown always means "already a binary", never "rebuild it": a multipart ETag, an unreadable CRAN index or an empty listing can never mass-schedule work. **A 20 h wall-clock budget** per shard. It exits 0, so the re-index and purge always fire and the remainder is picked up next run with no bookkeeping. **`.crow/weekly-rebuild-reindex.yaml`** takes over re-indexing and the purge, with `depends_on: [weekly-rebuild-missing]` and `runs_on: [success, failure]`. Three shards writing one slot's `PACKAGES` concurrently would race: `update_PACKAGES()` lists the live bucket, so an early lister that uploads last publishes an index missing its siblings' work. ## Verification `crow lint .crow/` passes on all 11 pipelines. `prek run` passes. 19 assertions in `local/tests/test-rebuild-missing.R`, 0 failures, covering the partition (disjoint, covering, deterministic, short lists, out-of-range index) and the outstanding filter (source ETag kept, binary ETag dropped, absent object kept, multipart and missing-from-CRAN treated as built). One of those tests caught a real bug before it shipped: an empty ETag table indexed to zero length rather than to `NA`, which recycled the result away and reported "nothing to build" — the dangerous direction. Fixed with an explicit `lookup()`. The filter run against the live `amd64/alpine324` index, using its `MD5sum` column as the ETag (established to match the objects): ``` index packages: 24343 outstanding (filter): 8950 no Built stamp: 8917 filter vs no-Built agreement: 8917 of 8917 outstanding but stamped Built: 33 (version drift vs CRAN) shard sizes: 2984/2983/2983 (sum 8950, unique 8950) ``` It reproduces the source-served set exactly. The extra 33 are packages whose slot version differs from CRAN's current one, so no object exists at the CRAN version key: correctly outstanding. ## Notes for review - The 20 h budget is a chosen default, exposed as `REBUILD_BUDGET_HOURS` in the pipeline. - `depends_on` is file-level, not row-level, so on a full cron run no slot is re-indexed until the slowest of all 54 jobs finishes. The budget bounds that at roughly a day. - An explicit cancel still skips the re-index. Recovery is to trigger `weekly-rebuild-reindex` on its own. - The purge runs on every re-index row rather than one designated slot: a cron fires only its own slot's row, so gating on a named slot would leave every other slot unpurged. - Out of scope: `build-all-versions` still cannot rebuild source fallbacks, because `local/build-all.R:113-122` drops every version with any `single_builds` row, which is precisely the source-fallback set. Design: `specs/2026-08-12-shard-weekly-rebuild-design.md` Reviewed-on: #163	2026-08-12 08:30:29 +00:00